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Volumn 130, Issue 12, 2009, Pages

Identification of the protein folding transition state from molecular dynamics trajectories

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; BOUNDARY CONDITIONS; DYNAMICS; FREE ENERGY; MOLECULAR DYNAMICS; TWO DIMENSIONAL;

EID: 63649158574     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3099705     Document Type: Article
Times cited : (33)

References (43)
  • 4
    • 0344301982 scopus 로고    scopus 로고
    • 1433-7851 10.1002/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3. 3.CO;2-8.
    • C. M. Dobson, A. Šali, and M. Karplus, Angew. Chem., Int. Ed. 1433-7851 10.1002/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3.3.CO;2- 8 37, 868 (1998).
    • (1998) Angew. Chem., Int. Ed. , vol.37 , pp. 868
    • Dobson, C.M.1    Šali, A.2    Karplus, M.3
  • 12
    • 33746567202 scopus 로고    scopus 로고
    • 1089-5647 10.1021/jp060039b.
    • S. V. Krivov and M. Karplus, J. Phys. Chem. B 1089-5647 10.1021/jp060039b 110, 12689 (2006).
    • (2006) J. Phys. Chem. B , vol.110 , pp. 12689
    • Krivov, S.V.1    Karplus, M.2
  • 17
    • 44849116304 scopus 로고    scopus 로고
    • 0006-3495 10.1529/biophysj.107.122606.
    • G. Settanni and A. Fersht, Biophys. J. 0006-3495 10.1529/biophysj.107. 122606 94, 4444 (2008).
    • (2008) Biophys. J. , vol.94 , pp. 4444
    • Settanni, G.1    Fersht, A.2
  • 19
    • 4143090730 scopus 로고    scopus 로고
    • 0022-2836 10.1016/j.jmb.2004.06.063.
    • F. Rao and A. Caflisch, J. Mol. Biol. 0022-2836 10.1016/j.jmb.2004.06.063 342, 299 (2004).
    • (2004) J. Mol. Biol. , vol.342 , pp. 299
    • Rao, F.1    Caflisch, A.2
  • 21
    • 1542345514 scopus 로고    scopus 로고
    • 0006-3495 10.1016/S0006-3495(04)74238-1.
    • G. Settanni, J. Gsponer, and A. Caflisch, Biophys. J. 0006-3495 10.1016/S0006-3495(04)74238-1 86, 1691 (2004).
    • (2004) Biophys. J. , vol.86 , pp. 1691
    • Settanni, G.1    Gsponer, J.2    Caflisch, A.3
  • 24
    • 33748374124 scopus 로고
    • 0021-9606 10.1063/1.436049.
    • D. Chandler, J. Chem. Phys. 0021-9606 10.1063/1.436049 68, 2959 (1978).
    • (1978) J. Chem. Phys. , vol.68 , pp. 2959
    • Chandler, D.1
  • 34
    • 0035946940 scopus 로고    scopus 로고
    • 0022-2836 10.1006/jmbi.2001.4552.
    • J. Gsponer and A. Caflisch, J. Mol. Biol. 0022-2836 10.1006/jmbi.2001. 4552 309, 285 (2001).
    • (2001) J. Mol. Biol. , vol.309 , pp. 285
    • Gsponer, J.1    Caflisch, A.2
  • 36
  • 37
    • 63649144230 scopus 로고    scopus 로고
    • See EPAPS Document No. E-JCPSA6-130-069912 for the supplementary material including explanations on the progress coordinate ZA /Z and cFEP with different progress variables, as well as the following supplementary figures: cFEP with x -axis transformed into mfpt (Fig. S1); normalized histograms of fold MD for the 34 nodes used for folding simulations (S2); pfoldf cFEP with an extra-node (S3); dependency of fold MD and fold N on τcommit (S4); distribution of number of native contacts (S5); results of the Markov state model with rmsd-based definition of boundary states (S6); correct TSE and putative TSE determined by fold N and fold MSM, respectively (S7); and histogram-based two-dimensional projection of the free energy (S8). For more information on EPAPS, see.
    • See EPAPS Document No. E-JCPSA6-130-069912 for the supplementary material including explanations on the progress coordinate ZA /Z and cFEP with different progress variables, as well as the following supplementary figures: cFEP with x -axis transformed into mfpt (Fig. S1); normalized histograms of p fold MD for the 34 nodes used for folding simulations (S2); pfoldf cFEP with an extra-node (S3); dependency of p fold MD and p fold N on τcommit (S4); distribution of number of native contacts (S5); results of the Markov state model with rmsd-based definition of boundary states (S6); correct TSE and putative TSE determined by p fold N and p fold MSM, respectively (S7); and histogram-based two-dimensional projection of the free energy (S8). For more information on EPAPS, see http://www.aip.org/pubservs/epaps.html.
  • 42
    • 17544374740 scopus 로고    scopus 로고
    • 1089-5647 10.1021/jp045546c.
    • A. Ma and A. R. Dinner, J. Phys. Chem. B 1089-5647 10.1021/jp045546c 109, 6769 (2005).
    • (2005) J. Phys. Chem. B , vol.109 , pp. 6769
    • Ma, A.1    Dinner, A.R.2


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